TRUA - BACSU - GREMLIN Contacts

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TRUA - tRNA pseudouridine synthase A

UniProt:	P70973	Sequences: MRLKCTISYDGHLFNGYQVQPGKRTVQDELEKALAVLHKSKDRIPVVSSGRTDSGVHAAGQVIHFDTPLSIPAERWPYALNALLPDDIAVKQAEIADDGFHARFSAVKKEYRYFVYTEKHPDVFKRHYAYHFSYRLNVQDMREAAKHLIGTHDFTSFCAAKTEVQDKVRTIYELDWTETADGLQMRITGSGFLYNMVRIIAGTLLDAGIGKISPDEVKSMLEAKDREAAGRTAPGHGLYLWNVYYDN	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	247 (242)
Sequences:	5652 (3986)
Seq/√Len:	256.2

ECOLI - TRUA
BACSU - TRUA
HALSA - TRUA

GREMLIN Results:

Legend: The darker and larger the blue dots, the higher coevolution strength.

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
155_T	167_K	3.014	1.00
108_K	244_Y	2.975	1.00
110_E	188_T	2.745	1.00
147_H	218_K	2.571	1.00
29_E	32_K	2.302	1.00
130_Y	205_L	2.296	1.00
156_S	223_A	2.284	1.00
108_K	188_T	2.254	1.00
151_T	170_T	2.237	1.00
19_V	31_E	2.132	1.00
142_R	146_K	2.098	1.00
15_N	23_K	2.098	1.00
218_K	222_E	2.097	1.00
110_E	186_R	2.082	1.00
212_I	216_E	2.074	1.00
28_D	32_K	2.061	1.00
24_R	29_E	2.029	1.00
13_L	87_D	1.953	1.00
112_R	241_W	1.917	1.00
112_R	184_Q	1.893	1.00
216_E	219_S	1.872	1.00
203_T	217_V	1.863	1.00
112_R	186_R	1.861	1.00
141_M	208_G	1.852	1.00
143_E	214_P	1.841	1.00
185_M	201_A	1.834	1.00
114_F	239_Y	1.803	1.00
77_P	93_A	1.798	1.00
27_Q	31_E	1.780	1.00
146_K	149_I	1.777	1.00
174_L	185_M	1.725	1.00
196_M	200_I	1.705	1.00
240_L	243_V	1.705	1.00
4_K	94_E	1.701	1.00
59_A	241_W	1.697	1.00
64_H	102_A	1.693	1.00
187_I	200_I	1.684	1.00
117_T	178_E	1.633	1.00
89_A	121_P	1.617	1.00
174_L	187_I	1.617	1.00
177_T	186_R	1.614	1.00
147_H	214_P	1.596	1.00
213_S	216_E	1.591	1.00
173_E	188_T	1.590	1.00
5_C	63_I	1.582	1.00
17_Y	63_I	1.574	1.00
36_V	83_L	1.561	1.00
108_K	172_Y	1.539	1.00
134_Y	209_I	1.538	1.00
14_F	87_D	1.538	1.00
171_I	187_I	1.533	1.00
145_A	174_L	1.525	1.00
14_F	24_R	1.516	1.00
35_A	43_R	1.487	1.00
4_K	62_V	1.476	1.00
110_E	244_Y	1.471	1.00
19_V	28_D	1.466	1.00
7_I	63_I	1.463	1.00
206_D	211_K	1.450	1.00
8_S	91_K	1.442	1.00
145_A	204_L	1.438	1.00
114_F	182_G	1.424	1.00
3_L	67_T	1.422	1.00
10_D	128_Y	1.420	1.00
24_R	87_D	1.408	1.00
137_N	210_G	1.393	1.00
12_H	127_H	1.375	1.00
137_N	140_D	1.355	1.00
3_L	93_A	1.352	1.00
203_T	230_G	1.324	1.00
172_Y	190_S	1.323	1.00
148_L	200_I	1.317	1.00
30_L	90_V	1.308	1.00
46_V	63_I	1.304	1.00
139_Q	142_R	1.301	1.00
114_F	184_Q	1.300	1.00
6_T	62_V	1.298	1.00
10_D	127_H	1.297	1.00
29_E	88_I	1.295	1.00
42_D	68_P	1.282	1.00
206_D	212_I	1.277	1.00
169_R	191_G	1.276	1.00
145_A	176_W	1.262	1.00
142_R	175_D	1.251	1.00
142_R	176_W	1.246	1.00
19_V	45_P	1.242	1.00
15_N	54_S	1.231	1.00
17_Y	48_S	1.226	1.00
172_Y	188_T	1.225	1.00
151_T	190_S	1.221	1.00
30_L	63_I	1.215	1.00
6_T	92_Q	1.215	1.00
115_V	185_M	1.203	1.00
107_V	246_D	1.201	1.00
12_H	57_H	1.185	1.00
13_L	127_H	1.172	1.00
195_N	199_I	1.168	1.00
140_D	210_G	1.166	1.00
9_Y	61_Q	1.144	1.00
110_E	241_W	1.144	1.00
188_T	244_Y	1.136	1.00
144_A	207_A	1.123	1.00
143_E	146_K	1.118	1.00
136_L	141_M	1.116	1.00
10_D	126_R	1.116	1.00
225_D	228_A	1.115	1.00
32_K	36_V	1.112	1.00
149_I	173_E	1.106	1.00
49_S	61_Q	1.104	1.00
122_D	125_K	1.098	1.00
130_Y	233_A	1.097	1.00
187_I	201_A	1.094	1.00
116_Y	129_A	1.091	1.00
151_T	168_V	1.079	1.00
6_T	60_G	1.071	1.00
220_M	223_A	1.067	1.00
125_K	182_G	1.063	1.00
223_A	228_A	1.063	1.00
158_C	167_K	1.062	1.00
31_E	46_V	1.060	1.00
138_V	178_E	1.058	1.00
122_D	129_A	1.057	1.00
130_Y	234_P	1.057	1.00
72_P	75_R	1.055	1.00
140_D	143_E	1.053	1.00
147_H	215_D	1.046	1.00
24_R	28_D	1.044	1.00
207_A	217_V	1.043	1.00
213_S	217_V	1.043	1.00
118_E	181_D	1.042	1.00
143_E	215_D	1.035	1.00
60_G	242_N	1.026	1.00
7_I	30_L	1.024	1.00
50_G	61_Q	1.023	1.00
176_W	185_M	1.022	1.00
110_E	242_N	1.022	1.00
96_A	99_G	1.017	1.00
101_H	104_F	1.008	1.00
138_V	183_L	1.003	1.00
140_D	214_P	1.001	1.00
15_N	25_T	0.999	1.00
177_T	184_Q	0.997	1.00
195_N	232_T	0.996	1.00
5_C	93_A	0.991	1.00
8_S	123_V	0.988	1.00
5_C	65_F	0.987	1.00
14_F	88_I	0.981	1.00
144_A	214_P	0.977	1.00
144_A	208_G	0.975	1.00
73_A	93_A	0.974	1.00
156_S	224_K	0.974	1.00
8_S	122_D	0.972	1.00
178_E	181_D	0.971	1.00
132_F	209_I	0.970	1.00
75_R	79_A	0.966	1.00
4_K	96_A	0.963	1.00
117_T	183_L	0.957	1.00
199_I	232_T	0.957	1.00
226_R	230_G	0.955	1.00
153_D	167_K	0.949	1.00
178_E	183_L	0.943	1.00
130_Y	236_H	0.941	1.00
47_V	64_H	0.941	1.00
205_L	233_A	0.939	1.00
128_Y	239_Y	0.936	1.00
14_F	26_V	0.935	1.00
25_T	28_D	0.934	1.00
141_M	204_L	0.933	1.00
159_A	195_N	0.933	1.00
140_D	213_S	0.930	1.00
174_L	204_L	0.929	1.00
115_V	205_L	0.916	1.00
37_L	83_L	0.911	1.00
142_R	178_E	0.908	1.00
174_L	200_I	0.904	1.00
4_K	100_F	0.904	1.00
6_T	94_E	0.898	1.00
49_S	243_V	0.894	1.00
157_F	220_M	0.893	1.00
80_L	90_V	0.893	1.00
187_I	197_V	0.892	1.00
176_W	183_L	0.876	1.00
175_D	186_R	0.869	1.00
26_V	88_I	0.864	1.00
73_A	95_I	0.861	1.00
138_V	142_R	0.856	0.99
75_R	78_Y	0.856	0.99
106_A	243_V	0.854	0.99
212_I	220_M	0.853	0.99
226_R	229_A	0.850	0.99
37_L	76_W	0.849	0.99
186_R	241_W	0.848	0.99
95_I	98_D	0.846	0.99
42_D	67_T	0.841	0.99
64_H	101_H	0.840	0.99
55_G	235_G	0.834	0.99
206_D	209_I	0.831	0.99
116_Y	122_D	0.831	0.99
44_I	65_F	0.827	0.99
129_A	182_G	0.821	0.99
125_K	129_A	0.816	0.99
34_L	65_F	0.813	0.99
202_G	230_G	0.813	0.99
158_C	162_T	0.812	0.99
109_K	191_G	0.810	0.99
148_L	217_V	0.804	0.99
148_L	174_L	0.802	0.99
38_H	67_T	0.798	0.99
173_E	186_R	0.798	0.99
158_C	161_K	0.797	0.99
215_D	219_S	0.797	0.99
132_F	205_L	0.795	0.99
219_S	228_A	0.793	0.99
176_W	204_L	0.792	0.99
161_K	194_Y	0.784	0.99
136_L	205_L	0.775	0.99
214_P	217_V	0.774	0.99
206_D	231_R	0.771	0.99
203_T	229_A	0.764	0.99
155_T	158_C	0.760	0.99
37_L	79_A	0.760	0.99
125_K	128_Y	0.760	0.99
48_S	63_I	0.760	0.99
38_H	44_I	0.752	0.99
15_N	22_G	0.751	0.99
34_L	80_L	0.751	0.99
81_N	89_A	0.750	0.99
7_I	17_Y	0.749	0.99
115_V	201_A	0.745	0.99
59_A	239_Y	0.739	0.98
49_S	245_Y	0.730	0.98
204_L	208_G	0.729	0.98
170_T	190_S	0.728	0.98
153_D	224_K	0.727	0.98
171_I	189_G	0.724	0.98
114_F	125_K	0.722	0.98
159_A	194_Y	0.722	0.98
139_Q	143_E	0.718	0.98
47_V	101_H	0.716	0.98
109_K	240_L	0.714	0.98
38_H	76_W	0.712	0.98
31_E	45_P	0.703	0.98
30_L	46_V	0.703	0.98
33_A	83_L	0.703	0.98
215_D	218_K	0.699	0.98
141_M	176_W	0.699	0.98
67_T	76_W	0.699	0.98
216_E	220_M	0.698	0.98
171_I	174_L	0.693	0.98
159_A	232_T	0.692	0.98
205_L	209_I	0.690	0.98
220_M	229_A	0.681	0.97
199_I	226_R	0.677	0.97
35_A	38_H	0.677	0.97
142_R	174_L	0.676	0.97
49_S	106_A	0.673	0.97
179_T	184_Q	0.673	0.97
14_F	29_E	0.669	0.97
29_E	33_A	0.668	0.97
17_Y	46_V	0.665	0.97
77_P	92_Q	0.665	0.97
156_S	225_D	0.664	0.97
50_G	240_L	0.663	0.97
115_V	183_L	0.661	0.97
113_Y	233_A	0.661	0.97
38_H	43_R	0.660	0.97
148_L	171_I	0.653	0.97
102_A	105_S	0.652	0.97
60_G	91_K	0.652	0.97
219_S	223_A	0.651	0.97
141_M	145_A	0.649	0.97
27_Q	46_V	0.648	0.97
144_A	204_L	0.642	0.96
6_T	91_K	0.638	0.96
74_E	78_Y	0.635	0.96
78_Y	82_A	0.633	0.96
147_H	217_V	0.633	0.96
138_V	176_W	0.629	0.96
220_M	230_G	0.626	0.96
63_I	90_V	0.624	0.96
50_G	243_V	0.624	0.96
34_L	38_H	0.620	0.96
199_I	229_A	0.618	0.96
117_T	132_F	0.617	0.95
124_F	128_Y	0.615	0.95
219_S	222_E	0.611	0.95
206_D	230_G	0.610	0.95
164_V	167_K	0.608	0.95
176_W	187_I	0.605	0.95
201_A	233_A	0.603	0.95
148_L	221_L	0.601	0.95
152_H	168_V	0.600	0.95
117_T	181_D	0.599	0.95
147_H	213_S	0.598	0.95
62_V	245_Y	0.596	0.95
116_Y	125_K	0.595	0.94
158_C	164_V	0.593	0.94
143_E	147_H	0.591	0.94
57_H	237_G	0.591	0.94
42_D	69_L	0.590	0.94
153_D	168_V	0.586	0.94
115_V	136_L	0.586	0.94
207_A	216_E	0.586	0.94
214_P	218_K	0.584	0.94
8_S	124_F	0.584	0.94
217_V	221_L	0.582	0.94
59_A	114_F	0.582	0.94
114_F	241_W	0.581	0.94
156_S	228_A	0.580	0.94
213_S	219_S	0.576	0.94
127_H	236_H	0.574	0.93
156_S	229_A	0.572	0.93
136_L	208_G	0.571	0.93
33_A	80_L	0.570	0.93
73_A	77_P	0.570	0.93
169_R	190_S	0.566	0.93
147_H	207_A	0.563	0.93
109_K	189_G	0.563	0.93
106_A	109_K	0.562	0.93
76_W	93_A	0.562	0.93
140_D	207_A	0.562	0.93
50_G	105_S	0.561	0.93
155_T	224_K	0.559	0.92
107_V	244_Y	0.558	0.92
241_W	244_Y	0.555	0.92
47_V	102_A	0.550	0.92
5_C	34_L	0.548	0.92
69_L	76_W	0.548	0.92
50_G	102_A	0.545	0.92
14_F	84_L	0.543	0.91
23_K	28_D	0.543	0.91
7_I	61_Q	0.541	0.91
35_A	44_I	0.540	0.91
109_K	195_N	0.538	0.91
77_P	120_H	0.534	0.91
189_G	199_I	0.532	0.91
85_P	88_I	0.531	0.90
19_V	32_K	0.531	0.90
156_S	220_M	0.528	0.90
203_T	220_M	0.528	0.90
3_L	95_I	0.527	0.90
101_H	245_Y	0.527	0.90
158_C	193_L	0.527	0.90
70_S	95_I	0.527	0.90
199_I	230_G	0.526	0.90
20_Q	25_T	0.524	0.90
128_Y	131_H	0.524	0.90
229_A	232_T	0.523	0.90
71_I	75_R	0.519	0.89
30_L	34_L	0.514	0.89
36_V	39_K	0.513	0.89
29_E	84_L	0.511	0.89
81_N	84_L	0.510	0.89
189_G	192_F	0.510	0.89
15_N	24_R	0.508	0.88
87_D	126_R	0.506	0.88
35_A	42_D	0.505	0.88
185_M	204_L	0.505	0.88
172_Y	189_G	0.504	0.88
39_K	69_L	0.503	0.88
149_I	152_H	0.503	0.88
13_L	24_R	0.502	0.88
38_H	69_L	0.500	0.88

Legend: The i and j are positions as given in the UniProt sequence. Only predictions with Prob ≥ 0.7 are listed. For all 3L/2 predictions, click on one of the links below.

Sco = ((raw_sco - min_sco)/(avg_sco - min_sco))/2 + 0.5
Prob = P(contact | Sco, seq80/√len)
seq80 = effective number of sequences, after reducing redundancy to 80% identity

Text file of predictions (all 3L/2 predictions)
Generate restraints for ROSETTA Structure Modeling
Upload PDB model overlay contacts on the model

HHsearch Results:

Legend: GREMLIN results (Prob ≥ 0.7) overlaid on top PDB hits. The grey/red filled circles underneath are pdb residue contacts (min distance < 5 Angstroms). The shade of the circles is based on the top 10 (or top 20 if e-value < 1E-20) HHsearch results which uses the overall probability and per-site alignment prob. Inter oligomeric contacts in the pdb are in shades of red.

PDB	Chains	Cov	%	HHΔ
1dj0A	2	0.9919	100	0.015	Contact Map
1vs3A	2	0.9838	100	0.024	Contact Map
4j37A	1	0.9514	100	0.076	Contact Map
2v9kA	1	0.8502	94.7	0.922	Contact Map
2l0cA	1	0.1336	11.6	0.965	Contact Map
1z2zA	1	0.9433	7.7	0.968	Contact Map
4kw3A	1	0.5101	6.5	0.969	Contact Map
4kt0E	1	0.1498	5.3	0.97	Contact Map
3rd4A	3	0.0972	5.1	0.971	Contact Map
1jb0E	1	0.1377	5.1	0.971	Contact Map

Sequence Conservation (Image Generated using WebLogo v3)

Legend: Color is used to show Hydrophobicity (Blue: Hydrophilic, Green: Neutral and Black: Hydrophobic). Amount of gaps is represented by width.

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